Long before Americans learned about the sexual escapades of their 20th-century presidents—Warren Harding, John Kennedy, and Bill Clinton were the chief offenders—there was the story of Thomas Jefferson and Sally Hemings. Until recently, when newly developed techniques in genetic research made scientific evidence on long-dead figures available to historians, the claim that Jefferson and his mulatto slave were sexual partners could be neither proved nor disproved. One historian described the story as “the longest-running mini-series in American history.” In January 2000 the Thomas Jefferson Memorial Foundation accepted the conclusion, supported by DNA evidence, that Jefferson and Hemings had at least one and probably six offspring between 1790 and 1808, though this conclusion was quickly and ardently contested by other individuals and groups.

The story has its origins in 1802, when a journalist of disreputable credentials, James Callender, published the initial accusation in The Richmond Recorder. Callender’s motives were hardly pure. Jefferson had hired him to libel John Adams in the presidential campaign of 1800, and Callender had then turned on Jefferson when the payment for his services did not include a political appointment. Rumours about miscegenation at Monticello had been making the rounds in Virginia for several years. They were based on the fact that an attractive house slave named Sally Hemings had several children who were obviously fathered by a white man and some of whom had features that resembled those of Jefferson. Neither Callender nor the Federalist editors who quickly picked up the story were primarily concerned if it was true. They were interested in using the scandal as a weapon to wound Jefferson, whose political stature was nearing its zenith.

In terms of practical political consequences, the charges proved ineffectual. Jefferson was reelected by a landslide in 1804, and the party he had founded dominated national politics almost unopposed for decades. But throughout the 19th century the “Tom and Sally” story, as it was then known, persisted as a titillating piece of innuendo that cast a shadow of doubt over Jefferson’s reputation in the history books.

Two new pieces of evidence surfaced in the 19th century, but they contradicted each other. In 1873 Madison Hemings, Sally’s next-to-last child (born in 1805), gave an interview to The Pike County (Ohio) Republican in which he claimed that Jefferson was his father and, in fact, the father of all of Sally’s five or six children. This claim was verified by Israel Jefferson, another ex-slave from Monticello and a longtime friend of Madison Hemings. The following year, James Parton published his Life of Thomas Jefferson and reported a story that had been circulating in the Jefferson and Randolph families for many years—namely, that Jefferson’s nephew, Peter Carr, when confronted by Martha Jefferson, had admitted that he was the father of all or most of Sally’s children.

There matters stood for nearly a century. The final piece of circumstantial evidence appeared in 1968 with the publication of Winthrop Jordan’s White Over Black: American Attitudes Toward the Negro, 1550–1812. Jordan noticed that Sally Hemings had become pregnant only when Jefferson was present at Monticello, a significant revelation because he was away fully two-thirds of the time. Jordan’s work also launched a new wave of scholarship that focused attention on Jefferson’s highly problematic status as a slave owner who harboured decidedly negative views on African Americans and strong convictions about the impossibility of any biracial American society. The more critical assessment of Jefferson’s character and legacy shed two different beams of light on the story of a sexual liaison with Sally Hemings. On one hand, it undercut the wholly reverential view of Jefferson, thereby making the charge even more plausible. On the other hand, it exposed the virulently racist values that Jefferson shared with other Virginia planters, thereby casting a new kind of doubt that he would engage in a long-term sexual relationship with a black woman. Over the next two decades scholarly opinion on the matter divided, though the majority of historians and biographers believed that the evidence remained inconclusive and unconvincing.

In November 1998 dramatic new scientific evidence became available. Several scholars had for many years advocated doing a DNA analysis of Jefferson’s remains and comparing the results with the descendants of Sally Hemings. But the white descendants of the Jefferson family had resisted the thought of digging up their ancestor as a ghoulish suggestion. And the likelihood of obtaining a sufficient sample of genetic material after so many years seemed remote. However, new techniques for matching parts of the male Y-chromosome made it possible to perform the comparison without actually getting the sample from Jefferson himself.

Because the Y-chromosome is passed intact on the male side, statistically reliable results could be obtained from any male descendant in the Jefferson family. Dr. Eugene Foster, a retired pathologist at the University of Virginia, gathered DNA samples from a living descendant of Jefferson’s paternal uncle, Field Jefferson, as well as from descendants of Sally’s youngest and eldest sons. The results revealed a perfect match between specific portions of Jefferson’s Y-chromosome and the Y-chromosome of Eston Hemings (born 1808). The chance of such a match occurring in a random sample is less than one in a thousand. The Foster study also included a comparison of the Hemings line with descendants of the Carr family, which showed no match, thereby undermining the explanation offered by Jefferson’s white descendants that Carr had fathered Sally’s children.

To be sure, the DNA evidence established probability rather than certainty. Several of Jefferson’s male relatives had the same Y-chromosome, making them equally genetically eligible as fathers, though none of them was present at Monticello nine months before each of Sally’s births, as Jefferson was. Nevertheless, those who most passionately contest Jefferson’s paternity can correctly argue that it is not a matter of scientific certainty. Whether Jefferson’s paternity has been proved beyond a reasonable doubt depends very much on who constitutes the jury.

Where does that leave us? Perhaps the best way to put it is to say that the burden of proof has shifted rather dramatically. The new scholarly consensus is that Jefferson and Hemings were sexual partners. How long the liaison lasted is less clear, though the burden of proof now rests on those who wish to reject the claim of Madison Hemings that the relationship was long-standing. The character of the relationship is even more a matter of conjecture. Whether it was consensual or coercive, a matter of love or rape, or perhaps a mutual arrangement that provided Jefferson with physical gratification and Hemings with privileged status and the promise of freedom for her children, is a matter of lively debate. That debate is likely to persist for some time, in part because the historical evidence is virtually nonexistent and in part because the question of Jefferson’s character has become a trophy in the culture wars. His admirers will be predisposed to interpret the liaison with Sally Hemings as a love affair, with Jefferson and Hemings cast in the role of America’s most preeminent biracial couple, or they will question the reliability of the DNA evidence, insisting that it is not scientifically conclusive or that it flies in the face of Jefferson’s character, at least as they perceive it. His critics will regard the relationship as symbolic of the predatory behaviour of white slaveholders and clinching evidence of Jefferson’s inveterate hypocrisy, which then expands to serve as a graphic illustration of the purely platitudinous character of his eloquent statements about human freedom and equality.